boltz-vsynthes 1.0.31__py3-none-any.whl → 1.0.33__py3-none-any.whl

boltz/data/parse/schema.py

@@ -2,6 +2,7 @@ from collections.abc import Mapping
 from dataclasses import dataclass
 from pathlib import Path
 from typing import Optional
+import json
 
 import click
 import numpy as np
@@ -1313,6 +1314,60 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
                 "cyclic", False
             ), "Cyclic flag is not supported for ligands"
 
+        elif (entity_type == "ligand") and ("sdf" in items[0][entity_type]):
+            # Handle SDF file
+            sdf_path = Path(items[0][entity_type]["sdf"])
+            from boltz.data.parse.sdf import parse_sdf
+            target = parse_sdf(sdf_path, ccd, mol_dir)
+            mol = target["sequences"][0]["ligand"]["smiles"]
+
+            if affinity:
+                mol = standardize(mol)
+
+            mol = AllChem.MolFromSmiles(mol)
+            mol = AllChem.AddHs(mol)
+
+            # Set atom names
+            canonical_order = AllChem.CanonicalRankAtoms(mol)
+            for atom, can_idx in zip(mol.GetAtoms(), canonical_order):
+                atom_name = atom.GetSymbol().upper() + str(can_idx + 1)
+                if len(atom_name) > 4:
+                    msg = (
+                        f"{mol} has an atom with a name longer than "
+                        f"4 characters: {atom_name}."
+                    )
+                    raise ValueError(msg)
+                atom.SetProp("name", atom_name)
+
+            success = compute_3d_conformer(mol)
+            if not success:
+                msg = f"Failed to compute 3D conformer for {mol}"
+                raise ValueError(msg)
+
+            mol_no_h = AllChem.RemoveHs(mol, sanitize=False)
+            affinity_mw = AllChem.Descriptors.MolWt(mol_no_h) if affinity else None
+            extra_mols[f"LIG{ligand_id}"] = mol_no_h
+            residue = parse_ccd_residue(
+                name=f"LIG{ligand_id}",
+                ref_mol=mol,
+                res_idx=0,
+            )
+
+            ligand_id += 1
+            parsed_chain = ParsedChain(
+                entity=entity_id,
+                residues=[residue],
+                type=const.chain_type_ids["NONPOLYMER"],
+                cyclic_period=0,
+                sequence=None,
+                affinity=affinity,
+                affinity_mw=affinity_mw,
+            )
+
+            assert not items[0][entity_type].get(
+                "cyclic", False
+            ), "Cyclic flag is not supported for ligands"
+
         else:
             msg = f"Invalid entity type: {entity_type}"
             raise ValueError(msg)
@@ -1371,15 +1426,43 @@ def parse_boltz_schema(  # noqa: C901, PLR0915, PLR0912
             protein_chains.add(chain_name)
 
         # Add affinity info
-        if chain.affinity and affinity_info is not None:
-            msg = "Cannot compute affinity for multiple ligands!"
-            raise ValueError(msg)
-
         if chain.affinity:
-            affinity_info = AffinityInfo(
-                chain_id=asym_id,
-                mw=chain.affinity_mw,
-            )
+            # If this is a protein binder, we need to create affinity info for each ligand
+            if chain_name in affinity_proteins:
+                # Find all ligand chains
+                ligand_chains = [
+                    (name, c) for name, c in chains.items() 
+                    if c.type == const.chain_type_ids["NONPOLYMER"]
+                ]
+                if not ligand_chains:
+                    msg = "No ligand chains found for protein binder!"
+                    raise ValueError(msg)
+                
+                # Create affinity info for each ligand
+                for ligand_name, ligand_chain in ligand_chains:
+                    affinity_info = AffinityInfo(
+                        chain_id=asym_id,
+                        mw=chain.affinity_mw,
+                    )
+                    # Save the affinity info in a subfolder named after the ligand
+                    output_dir = Path(f"output/{ligand_name}")
+                    output_dir.mkdir(parents=True, exist_ok=True)
+                    # Save the affinity info
+                    with open(output_dir / "affinity_info.json", "w") as f:
+                        json.dump({
+                            "chain_id": asym_id,
+                            "mw": chain.affinity_mw,
+                            "ligand_name": ligand_name
+                        }, f)
+            else:
+                # This is a ligand binder
+                if affinity_info is not None:
+                    msg = "Cannot compute affinity for multiple ligands!"
+                    raise ValueError(msg)
+                affinity_info = AffinityInfo(
+                    chain_id=asym_id,
+                    mw=chain.affinity_mw,
+                )
 
         # Find all copies of this chain in the assembly
         entity_id = int(chain.entity)

{boltz_vsynthes-1.0.31.dist-info → boltz_vsynthes-1.0.33.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: boltz-vsynthes
-Version: 1.0.31
+Version: 1.0.33
 Summary: Boltz for VSYNTHES
 Requires-Python: <3.13,>=3.10
 Description-Content-Type: text/markdown

{boltz_vsynthes-1.0.31.dist-info → boltz_vsynthes-1.0.33.dist-info}/RECORD

@@ -40,7 +40,7 @@ boltz/data/parse/mmcif.py,sha256=25kEXCkx-OuaawAs7cdz0fxdRu5_CCO0AV00u84PrjQ,368
 boltz/data/parse/mmcif_with_constraints.py,sha256=WHYZckSqUwu-Nb9vmVmxHmC7uxwVrF7AVUeVKsc5wGQ,51473
 boltz/data/parse/pdb.py,sha256=iybk4p2UgUy_ABGprDq_xxyPSdm1HAZsGTM0lhxVEwM,1654
 boltz/data/parse/pdb_download.py,sha256=wge-scX-lOatX0q83W1wOsaql99rYp-6uGWSHEc995M,2718
-boltz/data/parse/schema.py,sha256=9H7ZJpKb22KHXmfJAjG_0jz7VbZ1LAYt5eVp34_nwVw,62176
+boltz/data/parse/schema.py,sha256=5eU-_NR-g2XTtDpYXoREAy84DWTyHN8yRiXngd4BShs,65676
 boltz/data/parse/sdf.py,sha256=fs3MQVClDcCzxJaeVYiDuoh-fUrYc8Tcd5Bz8ws3FKI,2052
 boltz/data/parse/yaml.py,sha256=GRFRMtDD4PQ4PIpA_S1jj0vRaEu2LlZd_g4rN1zUrNo,1505
 boltz/data/sample/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -107,9 +107,9 @@ boltz/model/optim/scheduler.py,sha256=nB4jz0CZ4pR4n08LQngExL_pNycIdYI8AXVoHPnZWQ
 boltz/model/potentials/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 boltz/model/potentials/potentials.py,sha256=vev8Vjfs-ML1hyrdv_R8DynG4wSFahJ6nzPWp7CYQqw,17507
 boltz/model/potentials/schedules.py,sha256=m7XJjfuF9uTX3bR9VisXv1rvzJjxiD8PobXRpcBBu1c,968
-boltz_vsynthes-1.0.31.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
-boltz_vsynthes-1.0.31.dist-info/METADATA,sha256=4hMLLLOG2rXQo4bR4F_kU_jxyKnOVVQhrXiwwsHxDtk,7171
-boltz_vsynthes-1.0.31.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-boltz_vsynthes-1.0.31.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
-boltz_vsynthes-1.0.31.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
-boltz_vsynthes-1.0.31.dist-info/RECORD,,
+boltz_vsynthes-1.0.33.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
+boltz_vsynthes-1.0.33.dist-info/METADATA,sha256=XadtfwQoBLRNyaCe61wdMoCixayUE05BNfA7Y7hblgI,7171
+boltz_vsynthes-1.0.33.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+boltz_vsynthes-1.0.33.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
+boltz_vsynthes-1.0.33.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
+boltz_vsynthes-1.0.33.dist-info/RECORD,,